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Oliveira FR, Lansac-Tôha FM, Meira BR, Progênio M, Velho LFM. Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates. MICROBIAL ECOLOGY 2023; 87:10. [PMID: 38057381 DOI: 10.1007/s00248-023-02312-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/15/2023] [Indexed: 12/08/2023]
Abstract
Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.
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Affiliation(s)
- Felipe Rafael Oliveira
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Departamento de Biologia (DBI), Centro de Ciências Biológicas (CCB), Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupelia), Universidade Estadual de Maringá - UEM, Maringá, PR, 87020-900, Brazil.
- Faculdade de Ciências Agrárias e Biológicas (FACAB), Curso de Ciências Biológicas, Universidade do Estado do Mato Grosso - UNEMAT, 78.200-000, Cáceres, MT, Brazil.
| | - Fernando Miranda Lansac-Tôha
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Departamento de Biologia (DBI), Centro de Ciências Biológicas (CCB), Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupelia), Universidade Estadual de Maringá - UEM, Maringá, PR, 87020-900, Brazil
| | - Bianca Ramos Meira
- Instituto de Ciências Exatas e Biológicas, Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto - UFPO, Ouro Preto, MG, 35400-000, Brazil
| | - Melissa Progênio
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Departamento de Biologia (DBI), Centro de Ciências Biológicas (CCB), Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupelia), Universidade Estadual de Maringá - UEM, Maringá, PR, 87020-900, Brazil
| | - Luiz Felipe Machado Velho
- Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais (PEA), Departamento de Biologia (DBI), Centro de Ciências Biológicas (CCB), Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (Nupelia), Universidade Estadual de Maringá - UEM, Maringá, PR, 87020-900, Brazil
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Rondello Bonatti T, Vidal Siqueira-Castro IC, Averaldo Guiguet Leal D, Durigan M, Pedroso Dias RJ, Bueno Franco RM. Molecular characterization of waterborne protozoa in surface water and sediment in Brazil: a taxonomic survey of ciliated protozoa and their correlation with Giardia duodenalis and Cryptosporidium spp. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:470. [PMID: 36922479 DOI: 10.1007/s10661-023-11065-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The detection of Giardia duodenalis and Cryptosporidium spp. was performed, along with the identification of the ciliated protozoa biodiversity, to evaluate the correlation between these protozoa in freshwater quality monitoring. Water and sediment samples from two sites in the Atibaia River (Campinas, São Paulo, Brazil) were collected monthly for 2 years (n = 96). Pathogenic protozoa in water and sediment were detected by using immunomagnetic separation, followed by visualization by immunofluorescence assay (IFA). All positive aliquots in IFA were subjected to DNA extraction and subsequently nested PCR. Qualitative (in vivo observation and silver impregnation) and quantitative (in vivo enumeration) analyses were performed for the ciliated protozoa. Giardia cysts were detected in 62.5% of the surface water samples and Cryptosporidium spp. in 25.0%. In the sediment, cysts were detected in 35.4% samples and oocysts in 16.6%. A total of 57 samples positive for Giardia cysts were subjected to sequencing, 40 of which were harboring G. duodenalis (24 were characterized as sub-assemblage AII). For ciliated protozoa, 73 taxa belonging to 53 genera were identified over the period of the study. These results revealed a high degree of contamination by waterborne protozoa in the main water source which supplies drinking water for more than one million people in Campinas (São Paulo), highlighting the need for continuous monitoring of this catchment site. In addition, the present study provides important data regarding the sources of the water body degradation, i.e., fecal contamination of human origin, in addition to the survey of the ciliated protozoa.
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Affiliation(s)
- Taís Rondello Bonatti
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil.
| | - Isabel Cristina Vidal Siqueira-Castro
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil
| | | | - Maurício Durigan
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil
| | | | - Regina Maura Bueno Franco
- Laboratório de Protozoologia, Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, PO Box: 6109, CEP: 13083-970, São Paulo, Brazil
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Frantal D, Agatha S, Beisser D, Boenigk J, Darienko T, Dirren-Pitsch G, Filker S, Gruber M, Kammerlander B, Nachbaur L, Scheffel U, Stoeck T, Qian K, Weißenbacher B, Pröschold T, Sonntag B. Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution. Front Microbiol 2022; 12:787290. [PMID: 35185817 PMCID: PMC8854374 DOI: 10.3389/fmicb.2021.787290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.
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Affiliation(s)
- Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sabine Agatha
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Tatyana Darienko
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Experimental Phycology and Culture Collection of Algae, University of Göttingen, Göttingen, Germany
| | - Gianna Dirren-Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Sabine Filker
- Molecular Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | | | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- Federal Agency for Water Management, Institute for Aquatic Ecology and Fisheries Management, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Ulrike Scheffel
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Kuimei Qian
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- College of Environmental Engineering, Xuzhou University of Technology, Xuzhou, China
| | - Birgit Weißenbacher
- Department of Biosciences, Paris Lodron University of Salzburg, Salzburg, Austria
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
- *Correspondence: Bettina Sonntag,
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Rajter Ľ, Dunthorn M. Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.69602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.
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